Package: src:r-bioc-biocneighbors Version: 2.0.1+ds-3 Severity: serious Tags: ftbfs forky sid
Dear maintainer: During a rebuild of all packages in unstable, this package failed to build. Below you will find the last part of the build log (probably the most relevant part, but not necessarily). If required, the full build log is available here: https://people.debian.org/~sanvila/build-logs/202608/ About the archive rebuild: The build was made on virtual machines from AWS, using sbuild and a reduced chroot with only build-essential packages. If you cannot reproduce the bug please contact me privately, as I am willing to provide ssh access to a virtual machine where the bug is fully reproducible. If this is really a bug in one of the build-depends, please use reassign and add an affects on src:r-bioc-biocneighbors, so that this is still visible in the BTS web page for this package. Thanks. -------------------------------------------------------------------------------- [...] debian/rules clean dh clean --buildsystem R dh_auto_clean -O--buildsystem=R dh_autoreconf_clean -O--buildsystem=R dh_clean -O--buildsystem=R debian/rules binary dh binary --buildsystem R dh_update_autotools_config -O--buildsystem=R dh_autoreconf -O--buildsystem=R dh_auto_configure -O--buildsystem=R dh_auto_build -O--buildsystem=R dh_auto_test -O--buildsystem=R create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=R dh_prep -O--buildsystem=R dh_auto_install --destdir=debian/r-bioc-biocneighbors/ -O--buildsystem=R I: R Package: BiocNeighbors Version: 2.0.1 I: Building using R version 4.6.1-1 I: R API version: r-api-4.0 I: Using built-time from d/changelog: Fri, 13 Mar 2026 12:17:11 +0900 mkdir -p /<<BUILDDIR>>/r-bioc-biocneighbors-2.0.1\+ds/debian/r-bioc-biocneighbors/usr/lib/R/site-library R CMD INSTALL -l /<<BUILDDIR>>/r-bioc-biocneighbors-2.0.1\+ds/debian/r-bioc-biocneighbors/usr/lib/R/site-library --clean . --built-timestamp="'Fri, 13 Mar 2026 12:17:11 +0900'" * installing *source* package âBiocNeighborsâ ... ** this is package âBiocNeighborsâ version â2.0.1â file âinst/doc/userguide.htmlâ is missing ** using staged installation ** libs specified C++17 using C++ compiler: âx86_64-linux-gnu-g++ (Debian 16.1.0-3) 16.1.0â using C++17 make[1]: Entering directory '/<<PKGBUILDDIR>>/src' x86_64-linux-gnu-g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/usr/lib/R/site-library/Rcpp/include' -I'/usr/lib/R/site-library/assorthead/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: ../inst/include/BiocNeighbors.h:23:48: error: wrong number of template arguments (3, should be 2) 23 | typedef knncolle::SimpleMatrix<int, int, double> SimpleMatrix; | ^ In file included from /usr/lib/R/site-library/assorthead/include/knncolle/Builder.hpp:5, from /usr/lib/R/site-library/assorthead/include/knncolle/knncolle.hpp:4, from ../inst/include/BiocNeighbors.h:6: /usr/lib/R/site-library/assorthead/include/knncolle/Matrix.hpp:135:20: note: provided for âtemplate<class Index_, class Data_> class knncolle::SimpleMatrixâ 135 | class SimpleMatrix final : public Matrix<Index_, Data_> { | ^~~~~ ../inst/include/BiocNeighbors.h:28:47: error: wrong number of template arguments (2, should be at least 3) 28 | typedef knncolle::Builder<SimpleMatrix, double> Builder; | ^ /usr/lib/R/site-library/assorthead/include/knncolle/Builder.hpp:28:7: note: provided for âtemplate<class Index_, class Data_, class Distance_, class Matrix_> class knncolle::Builderâ 28 | class Builder { | ^~~~~~~ make[1]: *** [/usr/lib/R/etc/Makeconf:199: RcppExports.o] Error 1 make[1]: Leaving directory '/<<PKGBUILDDIR>>/src' make[1]: Entering directory '/<<PKGBUILDDIR>>/src' make[1]: Leaving directory '/<<PKGBUILDDIR>>/src' ERROR: compilation failed for package âBiocNeighborsâ * removing â/<<PKGBUILDDIR>>/debian/r-bioc-biocneighbors/usr/lib/R/site-library/BiocNeighborsâ dh_auto_install: error: R CMD INSTALL -l /<<BUILDDIR>>/r-bioc-biocneighbors-2.0.1\+ds/debian/r-bioc-biocneighbors/usr/lib/R/site-library --clean . --built-timestamp="'Fri, 13 Mar 2026 12:17:11 +0900'" returned exit code 1 make: *** [debian/rules:4: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2 --------------------------------------------------------------------------------
